Atomic force microscope kymograph analysis: A case study of two membrane proteins

Kymograph analysis is employed across the biological atomic force microscopy (AFM) community to boost temporal resolution. The method is well suited for revealing protein dynamics at the single molecule level in near-native conditions. Yet, kymograph analysis comes with limitations that depend on several factors including protein geometry and instrumental drift. This work focuses on conformational dynamics of difficult-to-study sparse distributions of membrane proteins. We compare and contrast AFM kymograph analysis for two proteins, one of which (SecDF) exhibits conformational dynamics primarily in the vertical direction (normal to the membrane surface) and the other (Pgp) exhibits a combination of lateral dynamics and vertical motion. Common experimental issues are analyzed including translational and rotational drift. Conformational transition detection is evaluated via kymograph simulations followed by state detection algorithms. We find that kymograph analysis is largely robust to lateral drift. Displacement of the AFM line scan trajectory away from the protein center of mass by a few nanometers, roughly half of the molecule diameter, does not significantly affect transition detection nor generate undue dwell time errors. On the other hand, for proteins like Pgp that exhibit significant azimuthal maximum height dependence, rotational drift can potentially produce artifactual transitions. Measuring the height of a membrane protein protrusion is generally superior to measurement of width, confirming intuition based on vertical resolution superiority. In low signal-to-noise scenarios, common state detection algorithms struggle with transition detection as opposed to infinite hidden Markov models. AFM kymography represents a valuable addition to the membrane biophysics toolkit; continued hardware and software improvements are poised to expand the method's impact in the field.

Value of high-speed videoendoscopy as an auxiliary tool in differentiation of benign and malignant unilateral vocal lesions

PURPOSE

The study aimed to assess the relevance of objective vibratory parameters derived from high-speed videolaryngoscopy (HSV) as a supporting tool, to assist clinicians in establishing the initial diagnosis of benign and malignant glottal organic lesions.

METHODS

The HSV examinations were conducted in 175 subjects: 50 normophonic, 85 subjects with benign vocal fold lesions, and 40 with early glottic cancer; organic lesions were confirmed by histopathologic examination. The parameters, derived from HSV kymography: amplitude, symmetry, and glottal dynamic characteristics, were compared statistically between the groups with the following ROC analysis.

RESULTS

Among 14 calculated parameters, 10 differed significantly between the groups. Four of them, the average resultant amplitude of the involved vocal fold (AmpInvolvedAvg), average amplitude asymmetry for the whole glottis and its middle third part (AmplAsymAvg; AmplAsymAvg_2/3), and absolute average phase difference (AbsPhaseDiffAvg), showed significant differences between benign and malignant lesions. Amplitude values were decreasing, while asymmetry and phase difference values were increasing with the risk of malignancy. In ROC analysis, the highest AUC was observed for AmpAsymAvg (0.719; p < 0.0001), and next in order was AmpInvolvedAvg (0.70; p = 0.0002).

CONCLUSION

The golden standard in the diagnosis of organic lesions of glottis remains clinical examination with videolaryngoscopy, confirmed by histopathological examination. Our results showed that measurements of amplitude, asymmetry, and phase of vibrations in malignant vocal fold masses deteriorate significantly in comparison to benign vocal lesions. High-speed videolaryngoscopy could aid their preliminary differentiation noninvasively before histopathological examination; however, further research on larger groups is needed.

Digital Videokymography: Analysis of Glottal Closure in Adults

INTRODUCTION

High-speed videolaryngoscopy and quantitative analysis of laryngeal images are relevant in accurately diagnosing vocal fold closure patterns.

OBJECTIVE

To analyze the parameters of digital videokymography obtained through high-speed videolaryngoscopy in women and men with complete and incomplete glottal closure, and posterior glottal chink.

METHODS

We conducted an observational, analytical, cross-sectional study with data from 65 adults, which we divided into groups according to sex and glottal closure. Digital videokymography parameters were analyzed using an image-processing program. The Anderson-Darling and Mann-Whitney U tests were used to verify sample normality and compare videokymography parameters between groups, respectively. The significance level was set at 5%.

RESULTS

Among 65 laryngeal images, 20 each were from women with complete and incomplete glottal closure, and 20 and 5 were from men with complete and incomplete glottal closure, respectively. Considering the clinical relevance of the evaluated data, groups of 11 women and 4 men with posterior glottal chink were compared with sex-similar groups with complete glottal closure. Digital videokymography showed a lower maximum and mean vocal fold opening in women with incomplete glottal closure, and a lower dominant left vocal fold-opening amplitude and higher dominant frequency of bilateral vocal fold opening in men with incomplete glottal closure. It also showed a lower closed phase percentage in the posterior region for women and men, with higher closed phase percentage in the anterior and middle regions in women. Both groups with posterior glottal chink showed similar results.

CONCLUSION

Incomplete glottal closure may interfere with the results of the digital videokymography parameters, with higher impact on the posterior vocal fold region in males and the middle and anterior vocal fold regions in females.

Interactions of tropomyosin Tpm1.1 on a single actin filament: A method for extraction and processing of high resolution TIRF microscopy data

Skeletal muscle tropomyosin (Tpm1.1) is an elongated, rod-shaped, alpha-helical coiled-coil protein that forms continuous head-to-tail polymers along both sides of the actin filament. In this study we use single molecule fluorescence TIRF microscopy combined with a microfluidic device and fluorescently labelled proteins to measure Tpm1.1 association to and dissociation from single actin filaments. Our experimental setup allows us to clearly resolve Tpm1.1 interactions on both sides of the filaments. Here we provide a semi-automated method for the extraction and quantification of kymograph data for individual actin filaments bound at different Tpm1.1 concentrations. We determine boundaries on the kymograph on each side of the actin filament, based on intensity thresholding, performing fine manual editing of the boundaries (if needed) and extracting user defined kinetic properties of the system. Using our analytical tools we can determine (i) nucleation point(s) and rates, (ii) elongation rates of Tpm1.1, (iii) identify meeting points after the saturation of filament, and when dissociation occurs, (iv) initiation point(s), (v) the final dissociation point(s), as well as (vi) dissociation rates.

All of these measurements can be extracted from both sides of the filament, allowing for the determination of possible differences in behaviour on the two sides of the filament, and across concentrations. The robust and repeatable nature of the method allows quantitative, semi-automated analyses to be made of large studies of acto-tropomyosin interactions, as well as for other actin binding proteins or filamentous structures, opening the way for dissection of the dynamics underlying these interactions.

Visual and Automatic Evaluation of Vocal Fold Mucosal Waves Through Sharpness of Lateral Peaks in High-Speed Videokymographic Images

INTRODUCTION

The sharpness of lateral peaks is a visually helpful clinical feature in high-speed videokymographic (VKG) images indicating vertical phase differences and mucosal waves on the vibrating vocal folds and giving insights into the health and pliability of vocal fold mucosa. This study aims at investigating parameters that can be helpful in objectively quantifying the lateral peak sharpness from the VKG images.

METHOD

Forty-five clinical VKG images with different degrees of sharpness of lateral peaks were independently evaluated visually by three raters. The ratings were compared to parameters obtained by automatic image analysis of the vocal fold contours: Open Time Percentage Quotients (OTQ) and Plateau Quotients (PQ). The OTQ parameters were derived as fractions of the period during which the vocal fold displacement exceeds a predetermined percentage of the vibratory amplitude. The PQ parameters were derived similarly but as a fraction of the open phase instead of a period.

RESULTS

The best correspondence between the visual ratings and the automatically derived quotients were found for the OTQ and PQ parameters derived at 95% and 80% of the amplitude, named OTQ₉₅, PQ₉₅, OTQ₈₀ and PQ₈₀. Their Spearman's rank correlation coefficients were in the range of 0.73 to 0.77 (P < 0.001) indicating strong relationships with the visual ratings. The strengths of these correlations were similar to those found from inter-rater comparisons of visual evaluations of peak sharpness.

CONCLUSION

The Open time percentage and Plateau quotients at 95% and 80% of the amplitude stood out as the possible candidates for capturing the sharpness of the lateral peaks with their reliability comparable to that of visual ratings.

[High-speed digital imaging in the clinical analysis of voice change as a parameter of premenstrual syndrome]

Technique of high-speed digital imaging (HSDI) is unique technology, allowing assessment of real vocal fold vibrations.

AIM

The aim of the study is to present the usefulness of HSDI in the diagnosis of premenstrual dysphonia as a parameter of premenstrual syndrome (PMS).

MATERIALS AND METHODS

In study conducted by Department of Clinical Phonoaudiology and Logopedics at the Medical University of Białystok participated 21 women aged between 20-31 years old. HSDI technique with a digital High Speed HS camera was used for visualization of the larynx. The rigid endoscope with 90° optics was used for visualizing the vocal folds vibrations during phonation of "e" vowel, at the rate of 4000 frames per second. Playback of recorded sequence set at 15 frames per second, allowed to assess vocal folds vibrations in slow motion mode. Mucosal wave (MW), glottal closure (GTs), symmetry, regularity and synchrony of vocal fold vibration were analyzed. Kymography of the larynx was made for analyzing the value of the Open Quotient (OQ) in the assessment of degree of glottal insufficiency. Study was conducted in the follicular phase of the menstrual cycle and then repeated 2-3 days before menstruation.

RESULTS

In the analyzed group of patients studied before menstruation only 19% of women complained of hoarseness and fatigue of voice, and 81% reported no problems with his voice but the edematous changes in the larynx was recorded by HSDI technique. No women had premenstrual dysphonia in the follicular phase of the menstrual cycle.

CONCLUSIONS

HSDI allows objective assessment of the degree of severity of insufficiency of glottal closure and edematous changes in the vocal folds in premenstrual dysphonia, what is confirmed by the objective values of the OQ.

Effect of level difference between left and right vocal folds on phonation: Physical experiment and theoretical study

As an alternative factor to produce asymmetry between left and right vocal folds, the present study focuses on level difference, which is defined as the distance between the upper surfaces of the bilateral vocal folds in the inferior-superior direction. Physical models of the vocal folds were utilized to study the effect of the level difference on the phonation threshold pressure. A vocal tract model was also attached to the vocal fold model. For two types of different models, experiments revealed that the phonation threshold pressure tended to increase as the level difference was extended. Based upon a small amplitude approximation of the vocal fold oscillations, a theoretical formula was derived for the phonation threshold pressure. This theory agrees with the experiments, especially when the phase difference between the left and right vocal folds is not extensive. Furthermore, an asymmetric two-mass model was simulated with a level difference to validate the experiments as well as the theory. The primary conclusion is that the level difference has a potential effect on voice production especially for patients with an extended level of vertical difference in the vocal folds, which might be taken into account for the diagnosis of voice disorders.

The relation between tongue shape and pitch in clarinet playing using ultrasound measurements

Tongue shapes during clarinet performances of chromatic scale, portamento and pitch bending exercises were imaged using an ultrasound machine while audio and video were recorded synchronously. Analysis of the data from four participants revealed that tongue position varies non-monotically with note frequency in the lowest register (up to ≈ 440 Hz) and then descends monotonically as note frequencies rise through the upper registers. The descent of the tongue results in an expansion of the vocal tract's posterior oral cavity, resulting in a vocal tract input impedance maximum tuned to high frequency. Portamento and pitch bending were found to involve a raising of the tongue and concomitant contraction of the posterior oral cavity. The degree of contraction was similar in both portamento and pitch bending, suggesting a common acoustic mechanism.

Characterization of Vocal Fold Vibration in Sulcus Vocalis Using High-Speed Digital Imaging

PURPOSE

The aim of the present study was to qualitatively and quantitatively characterize vocal fold vibrations in sulcus vocalis by high-speed digital imaging (HSDI) and to clarify the correlations between HSDI-derived parameters and traditional vocal parameters.

METHOD

HSDI was performed in 20 vocally healthy subjects (8 men and 12 women) and 41 patients with sulcus vocalis (33 men and 8 women). Then HSDI data were evaluated by assessing the visual-perceptual rating, digital kymography, and glottal area waveform.

RESULTS

Patients with sulcus vocalis frequently had spindle-shaped glottal gaps and a decreased mucosal wave. Compared with the control group, the sulcus vocalis group showed higher open quotient as well as a shorter duration of the visible mucosal wave, a smaller speed index, and a smaller glottal area difference index ([maximal glottal area - minimal glottal area]/maximal glottal area). These parameters deteriorated in order of the control group and Type I, II, and III sulcus vocalis. There were no gender-related differences. Strong correlations were noted between the open quotient and the type of sulcus vocalis.

CONCLUSIONS

HSDI was an effective method for documenting the characteristics of vocal fold vibrations in patients with sulcus vocalis and estimating the severity of dysphonia.

Synthetic multi-line kymographic analysis: A spatiotemporal data reduction technique for high-speed videoendoscopy

High-speed videoendoscopy (HSV) enables observation of the true vibratory behavior of the vocal folds. To quantify the vocal fold vibration captured by the HSV, lateral movement features (e.g., glottal width and vocal fold edge displacements) have been extracted as functions of time. The most common analysis method is to extract the features on a lateral strip used to form digital kymogram. The weakness of this method is that it can only capture the vibrational behavior local to the strip location. While the multi-line kymographic approach has been utilized to capture the spatial diversity, the observation points are either fixed or manually positioned. Behaviors of pathological vocal folds, especially those with lesions, are expected to be spatially diverse and also diverse among speakers, making fixed observation points ineffective. This paper proposes a technique to synthesize kymographic waveforms from full spatiotemporal HSV feature data to extract distinctive behaviors automatically. Each synthesized waveform represents a non-overlapping section of the glottis, where vocal folds are locally behaving homogeneously. The efficacy of the algorithm is demonstrated with four HSV recordings (three pathological) and discussed, including mitigation of the known drawbacks.

[High-speed digital imaging in the diagnosis of voice pathologies]

Technique of high-speed digital imaging (HSDI) is unique technique, allowing for assessment of real vocal fold vibrations.

AIM

The aim of the study is to present the usefulness of HSDI in the diagnosis of clinical type of dysphonia.

MATERIALS AND METHODS

The study group was diagnosed at the Department of Clinical Phonoaudiology and Logopedics at the Medical University of Białystok and treated at the Phoniatric Clinic in years 2012-2015. HSDI technique with a digital camera was used for visualization of the larynx. The rigid endoscope with 90° optics was used for visualizing the vocal folds vibrations during phonation of "e" vowel, at the rate of 4000 frames per second. Playback of recorded sequence set at 15 frames per second, what allowed to assess vocal folds vibrations in slow motion mode during over 8 minutes. Mucosal wave (MW), glottal closure, symmetry, regularity and synchrony of vocal fold vibration were analyzed. Digital kymography (DKG) of the larynx was made for analyzing the value of the Open Quotient (OQ) in the assessment of degree of glottal insufficiency.

RESULTS

In the analyzed group of patients, the functional dysphonia was diagnosed in 71%, organic dysphonia in 29% patients. In 68%, glottal insufficiency was registered in the rear part at the glottis. The oedematous-hypertrophic changes were diagnosed in 21% of the cases, hypertrophic changes of larynx - in 6%, vocal fold polyps - in 3% and vocal fold nodules - in 2% of patients.

CONCLUSIONS

Examination of the larynx by using HSDI technique is quick, non-invasive to patient. HSDI allows to objective assessment of the degree of severity of insufficiency of glottal closure, what is confirmed by the objective values of the OQ. Evaluation of MW allows for the differentiation of clinical type and severity of organic dysphonia.

[Direct and indirect mucosal wave imaging techniques]

The vocal folds play a key role in the process of phonation. Cyclical movements of the vocal folds model a space called glottis, what leads to voice formation. The space contains surface between the vocal folds and the inner surface of the arytenoid cartilages. The best indicator of the vocal folds vibratory function is the mucosal wave. The presence and size of the mucosal wave is widely recognized as an indicator of tension and plasticity of vocal folds. It is also essential in the process of creating a proper, resonant voice. In the article, current knowledge of mucosal wave imaging techniques is given. Imaging can be carried out directly and indirectly. Among the direct methods, the following are distinguished: laryngostroboscopy, laryngovideostroboscopy, videokymography and high-speed digital imaging. Indirect methods include: electroglottography, photoglottography and ultrasonography.

Heat stress affects the cytoskeleton and the delivery of sucrose synthase in tobacco pollen tubes

MAIN CONCLUSION

Heat stress changes isoform content and distribution of cytoskeletal subunits in pollen tubes affecting accumulation of secretory vesicles and distribution of sucrose synthase, an enzyme involved in cell wall synthesis. Plants are sessile organisms and are therefore exposed to damages caused by the predictable increase in temperature. We have analyzed the effects of temperatures on the development of pollen tubes by focusing on the cytoskeleton and related processes, such as vesicular transport and cell wall synthesis. First, we show that heat stress affects pollen germination and, to a lesser extent, pollen tube growth. Both, microtubules and actin filaments, are damaged by heat treatment and changes of actin and tubulin isoforms were observed in both cases. Damages to actin filaments mainly concern the actin array present in the subapex, a region critical for determining organelle and vesicle content in the pollen tube apex. In support of this, green fluorescent protein-labeled vesicles are arranged differently between heat-stressed and control samples. In addition, newly secreted cell wall material (labeled by propidium iodide) shows an altered distribution. Damage induced by heat stress also extends to proteins that bind actin and participate in cell wall synthesis, such as sucrose synthase. Ultimately, heat stress affects the cytoskeleton thereby causing alterations in the process of vesicular transport and cell wall deposition.

Behavior of Kinesin Driven Quantum Dots Trapped in a Microtubule Loop

We report the observation of kinesin driven quantum dots (QDs) trapped in a microtubule loop, allowing the investigation of moving QDs for a long time and an unprecedented long distance. The QD conjugates did not depart from our observational field of view, enabling the tracking of specific conjugates for more than 5 min. The unusually long run length and the periodicity caused by the loop track allow comparing and studying the trajectory of the kinesin driven QDs for more than 2 full laps, i.e., about 70 μm, enabling a statistical analysis of interactions of the same kinesin driven object with the same obstacle. The trajectories were extracted and analyzed from kymographs with a newly developed algorithm. Despite dispersion, several repetitive trajectory patterns can be identified. A method evaluating the similarity is introduced allowing a quantitative comparison between the trajectories. The velocity variations appear strongly correlated to the presence of obstacles. We discuss the reasons making this long continuous travel distances on the loop track possible.

Direct Measurements of Local Coupling between Myosin Molecules Are Consistent with a Model of Muscle Activation

Muscle contracts due to ATP-dependent interactions of myosin motors with thin filaments composed of the proteins actin, troponin, and tropomyosin. Contraction is initiated when calcium binds to troponin, which changes conformation and displaces tropomyosin, a filamentous protein that wraps around the actin filament, thereby exposing myosin binding sites on actin. Myosin motors interact with each other indirectly via tropomyosin, since myosin binding to actin locally displaces tropomyosin and thereby facilitates binding of nearby myosin. Defining and modeling this local coupling between myosin motors is an open problem in muscle modeling and, more broadly, a requirement to understanding the connection between muscle contraction at the molecular and macro scale. It is challenging to directly observe this coupling, and such measurements have only recently been made. Analysis of these data suggests that two myosin heads are required to activate the thin filament. This result contrasts with a theoretical model, which reproduces several indirect measurements of coupling between myosin, that assumes a single myosin head can activate the thin filament. To understand this apparent discrepancy, we incorporated the model into stochastic simulations of the experiments, which generated simulated data that were then analyzed identically to the experimental measurements. By varying a single parameter, good agreement between simulation and experiment was established. The conclusion that two myosin molecules are required to activate the thin filament arises from an assumption, made during data analysis, that the intensity of the fluorescent tags attached to myosin varies depending on experimental condition. We provide an alternative explanation that reconciles theory and experiment without assuming that the intensity of the fluorescent tags varies.

Despite decades of study, there is no clear connection between muscle contraction at the molecular and the macroscopic scale. For example, we cannot yet predict how a genetic defect in a muscle protein will result in a physiological change in the heart. This multi-scale understanding is difficult, in part, because molecules cooperate during muscle contraction; that is, one molecule’s behavior is influenced by the behavior of its neighbors. It is difficult to make direct measurements from such coupled molecular systems and also difficult to describe them quantitatively. Despite these obstacles, we recently published experimental measurements and theoretical models of this coupling, but there were apparent discrepancies between the two. Here, we use detailed computer simulations of these experiments to show that, in fact, the measurements agree with the model to a remarkable extent. This agreement suggests that the model captures the essential molecular events that underlie the coupling between muscle molecules. This removes a major obstacle to a multi-scale understanding of muscle contraction and, while more work is necessary, suggests that a connection between the molecular and macroscopic scale is within reach.

Leaf movements and their relationship with the lunisolar gravitational force

BACKGROUND

Observation of the diurnal ascent and descent of leaves of beans and other species, as well as experimental interventions into these movements, such as exposures to light at different times during the movement cycle, led to the concept of an endogenous 'clock' as a regulator of these oscillations. The physiological basis of leaf movement can be traced to processes that modulate cell volume in target tissues of the pulvinus and petiole. However, these elements of the leaf-movement process do not completely account for the rhythms that are generated following germination in constant light or dark conditions, or when plants are transferred to similar free-running conditions.

SCOPE

To develop a new perspective on the regulation of leaf-movement rhythms, many of the published time courses of leaf movements that provided evidence for the concept of the endogenous clock were analysed in conjunction with the contemporaneous time courses of the lunisolar tidal acceleration at the relevant experimental locations. This was made possible by application of the Etide program, which estimates, with high temporal resolution, local gravitational changes as a consequence of the diurnal variations of the lunisolar gravitational force due to the orbits and relative positions of Earth, Moon and Sun. In all cases, it was evident that a synchronism exists between the times of the turning points of both the lunisolar tide and of the leaftide when the direction of leaf movement changes. This finding of synchrony leads to the hypothesis that the lunisolar tide is a regulator of the leaftide, and that the rhythm of leaf movement is not necessarily of endogenous origin but is an expression of an exogenous lunisolar 'clock' impressed upon the leaf-movement apparatus.

CONCLUSIONS

Correlation between leaftide and Etide time courses holds for leaf movement rhythms in natural conditions of the greenhouse, in conditions of constant light or dark, under microgravity conditions of the International Space Station, and also holds for rhythms that are atypical, such as pendulum and relaxation rhythms whose periods are longer or shorter than usual. Even the apparently spontaneous short-period, small-amplitude rhythms recorded from leaves under unusual growth conditions are consistent with the hypothesis of a lunisolar zeitgeber. Two hypotheses that could account for the synchronism between leaftide and Etide, and which are based on either quantum considerations or on classical Newtonian physics, are presented and discussed.

Laryngeal flow due to longitudinal sweeping motion of the vocal folds and its contribution to auto-oscillation

Analysis of published depth-kymography data [George, de Mul, Qiu, Rakhorst, and Schutte (2008). Phys. Med. Biol. 53, 2667-2675] shows that, for the subject studied, the flow due to the longitudinal sweeping motion of the vocal folds contributes several percent of a typical acoustic flow at the larynx. This sweeping flow is a maximum when the glottis is closed. This observation suggests that assumption of zero laryngeal flow during the closed phase as a criterion when determining parameters in inverse filtering should be used with caution. Further, these data suggest that the swinging motion contributes work to overcome mechanical losses and thus to assist auto-oscillation.

Glottal Adduction and Subglottal Pressure in Singing

Previous research suggests that independent variation of vocal loudness and glottal configuration (type and degree of vocal fold adduction) does not occur in untrained speech production. This study investigated whether these factors can be varied independently in trained singing and how subglottal pressure is related to average glottal airflow, voice source properties, and sound level under these conditions. A classically trained baritone produced sustained phonations on the endoscopic vowel [i:] at pitch D4 (approximately 294 Hz), exclusively varying either (a) vocal register; (b) phonation type (from "breathy" to "pressed" via cartilaginous adduction); or (c) vocal loudness, while keeping the others constant. Phonation was documented by simultaneous recording of videokymographic, electroglottographic, airflow and voice source data, and by percutaneous measurement of relative subglottal pressure. Register shifts were clearly marked in the electroglottographic wavegram display. Compared with chest register, falsetto was produced with greater pulse amplitude of the glottal flow, H1-H2, mean airflow, and with lower maximum flow declination rate (MFDR), subglottal pressure, and sound pressure. Shifts of phonation type (breathy/flow/neutral/pressed) induced comparable systematic changes. Increase of vocal loudness resulted in increased subglottal pressure, average flow, sound pressure, MFDR, glottal flow pulse amplitude, and H1-H2. When changing either vocal register or phonation type, subglottal pressure and mean airflow showed an inverse relationship, that is, variation of glottal flow resistance. The direct relation between subglottal pressure and airflow when varying only vocal loudness demonstrated independent control of vocal loudness and glottal configuration. Achieving such independent control of phonatory control parameters would be an important target in vocal pedagogy and in voice therapy.

Oscillations of Min-proteins in micropatterned environments: a three-dimensional particle-based stochastic simulation approach

The Min-proteins from E. coli and other bacteria are the best characterized pattern forming system in cells and their spatiotemporal oscillations have been successfully reconstituted in vitro. Different mathematical and computational models have been used to better understand these oscillations. Here we use particle-based stochastic simulations to study Min-oscillations in patterned environments. We simulate a rectangular box of length 10 μm and width 5 μm that is filled with grid or checkerboard patterns of different patch sizes and distances. For this geometry, we find different stable oscillation patterns, typically pole-to-pole oscillations along the minor axis and striped oscillations along the major axis. The Min-oscillations can switch from one pattern to the other, either effected by changes in pattern geometry or stochastically. By automatic analysis of large-scale computer simulations, we show quantitatively how the perturbing effect of increased patch distance can be rescued by increased patch size. We also show that striped oscillations occur robustly in arbitrarily shaped filamentous E. coli cells. Our results highlight the robustness and variability of Min-oscillations, put limits on the effect of putative division sites, and provide a powerful computational framework for future studies of protein self-organization in patterned environments.

Computational modeling reveals optimal strategy for kinase transport by microtubules to nerve terminals

Intracellular transport of proteins by motors along cytoskeletal filaments is crucial to the proper functioning of many eukaryotic cells. Since most proteins are synthesized at the cell body, mechanisms are required to deliver them to the growing periphery. In this article, we use computational modeling to study the strategies of protein transport in the context of JNK (c-JUN NH2-terminal kinase) transport along microtubules to the terminals of neuronal cells. One such strategy for protein transport is for the proteins of the JNK signaling cascade to bind to scaffolds, and to have the whole protein-scaffold cargo transported by kinesin motors along microtubules. We show how this strategy outperforms protein transport by diffusion alone, using metrics such as signaling rate and signal amplification. We find that there exists a range of scaffold concentrations for which JNK transport is optimal. Increase in scaffold concentration increases signaling rate and signal amplification but an excess of scaffolds results in the dilution of reactants. Similarly, there exists a range of kinesin motor speeds for which JNK transport is optimal. Signaling rate and signal amplification increases with kinesin motor speed until the speed of motor translocation becomes faster than kinase/scaffold-motor binding. Finally, we suggest experiments that can be performed to validate whether, in physiological conditions, neuronal cells do indeed adopt such an optimal strategy. Understanding cytoskeletal-assisted protein transport is crucial since axonal and cell body accumulation of organelles and proteins is a histological feature in many human neurodegenerative diseases. In this paper, we have shown that axonal transport performance changes with altered transport component concentrations and transport speeds wherein these aspects can be modulated to improve axonal efficiency and prevent or slowdown axonal deterioration.

Visual assessment of voice disorders in patients with occupational dysphonia

INTRODUCTION

In a group of persons using the voice occupationally, the frequent symptoms are hoarseness, voice fatigability and aphonia. Pathological changes in the larynx may have organic or functional character which require different methods of treatment and rehabilitation. Visualization of vibrations of the vocal folds is an essential condition for an appropriate assessment of the causes of dysphonia.

OBJECTIVE

The purpose of the study is assessment of the usefulness of a high-speed imaging (HSI) system in the diagnosis of functional and organic dysphonia of occupational character, compared with digital kymography (DKG) and digital stroboscopy (DS) with a high resolution module.

MATERIAL AND METHODS

The study group consisted of 64 patients with voice quality disorders with features of occupational dysphonia. The control group consisted of 15 patients with euphonic voice. Analysis of the voice quality parameters during phonation of the 'e' vowel was performed using HSI, DKG and stroboscopy of high resolution, by means of a digital HS camera (HRES Endocam, Richard Wolf GmbH, Knittlingen, Germany). Vocal folds vibrations were registered at the rate of 4,000 frames per second.

RESULTS

HSI is the most reliable diagnostic tool giving the possibility of an analysis of the true vibrations of the vocal folds. It also enables an observation of the aperiodicity of vibrations of the vocal folds, while DS with high resolution allows diagnosis of the periodicity of the vibrations.

CONCLUSIONS

HSI is particularly useful in the diagnosis of neurologically-based pathology of the voice (paralytic dysphonia) and organic dysphonia. The quickest method of diagnosing the phonatory paresis of the glottis is DKG. The advantage of both HSI and DKG is the non-invasiveness of examinations; however, their limitations are time-consuming and the high cost of equipment.

On the acoustic effects of the supraglottic structures in excised larynges

The acoustic effects of the supraglottic laryngeal structures (SGSs), including the false vocal folds (FVFs) laryngeal ventricle, and the epiglottis were investigated in an excised canine larynx model with and without these anatomical structures. The purpose of this study was to better understand the acoustic contributions of these structures to phonation. Canine larynges were prepared and mounted over a 3/4 in. tube, which supplied pressurized, heated, and humidified air. Glottal adduction was accomplished by rotating the arytenoids with a suture passed behind the vocal folds to simulate the lateral cricoarytenoid muscle action. The SGSs were kept intact in the first part of the experiment and were removed in the second part. Results indicated that when the FVFs vibrated, a low frequency component was observed in the spectral data. The excised larynx with a SGS had a limited range of frequency with subglottal pressure, while the larynx without a SGS had a larger frequency range. The excised canine larynx with a SGS oscillated with a higher phonation threshold pressure and significantly louder.

Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria

BACKGROUND

Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this approach to other species of bacteria, many of whom have dimensions in the sub-micron range, or to a larger range of growth conditions, a readily-fabricated device containing sub-micron features is required.

RESULTS

Here we detail the fabrication of a versatile device with growth channels whose widths range from 0.3 μm to 0.8 μm. The device is fabricated using electron beam lithography, which provides excellent control over the shape and size of different growth channels and facilitates the rapid-prototyping of new designs. Features are successfully transferred first into silicon, and subsequently into the polydimethylsiloxane that forms the basis of the working microfluidic device. We demonstrate that the growth of sub-micron scale bacteria such as Lactococcus lactis or Escherichia coli cultured in minimal medium can be followed in such a device over several generations.

CONCLUSIONS

We have presented a detailed protocol based on electron beam fabrication together with specific dry etching procedures for the fabrication of a microfluidic device suited to study submicron-sized bacteria. We have demonstrated that both Gram-positive and Gram-negative bacteria can be successfully loaded and imaged over a number of generations in this device. Similar devices could potentially be used to study other submicron-sized organisms under conditions in which the height and shape of the growth channels are crucial to the experimental design.

In vivo imaging of IFT in Chlamydomonas flagella

Intraflagellar transport (IFT) is a specialized intracellular transport which is required for the assembly and maintenance of cilia and eukaryotic flagella. IFT protein particles move bidirectionally along the flagella in the space between the flagellar membrane and the axonemal doublets. The particles consist of more than 20 different polypeptides and are transported by kinesin-2 from the cell body to the flagellar tip and by cytoplasmic dynein back to the cell body. Chlamydomonas reinhardtii is unique in that IFT can be visualized by two distinct microscopic approaches: differential interference contrast (DIC) and tracking of fluorescently tagged IFT proteins. In vivo imaging of IFT is critical to determine, for example, the role of individual proteins in the IFT pathway and how flagellar proteins are transported by IFT. Here, the microscopic requirements and the procedures for the imaging of IFT by DIC and by total internal reflection fluorescence microscopy will be described. Kymograms, graphical representations of spatial position over time, provide a convenient way to analyze in vivo recordings of IFT. In the future, multicolor in vivo imaging of IFT and its cargoes will be used to understand how flagella are assembled, maintained, and repaired.

Visualization of live primary cilia dynamics using fluorescence microscopy

Methods useful for exploring the formation and functions of primary cilia in living cells are described here. First, multiple protocols for visualizing solitary cilia that extend away from the cell body are described. Primary cilia collect, synthesize, and transmit information about the extracellular space into the cell body to promote critical cellular responses. Problems with cilia formation or function can lead to dramatic changes in cell physiology. These methods can be used to assess cilia formation and length, the location of the cilium relative to other cellular structures, and localization of specific proteins to the cilium. The subsequent protocols describe how to quantify movement of fluorescent molecules within the cilium using kymographs, photobleaching, and photoconversion. The microtubules that form the structural scaffold of the cilium are also critical avenues for kinesin and dynein-mediated movement of proteins within the cilium. Assessing intraflagellar dynamics can provide insight into mechanisms of ciliary-mediated signal perception and transmission.

Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold

Cytoplasmic dynein and kinesin-1 are microtubule-based motors with opposite polarity that transport a wide variety of cargo in eukaryotic cells. Many cellular cargos demonstrate bidirectional movement due to the presence of ensembles of dynein and kinesin, but are ultimately sorted with spatial and temporal precision. To investigate the mechanisms that coordinate motor ensemble behavior, we built a programmable synthetic cargo using three-dimensional DNA origami to which varying numbers of DNA oligonucleotide-linked motors could be attached, allowing for control of motor type, number, spacing, and orientation in vitro. In ensembles of one to seven identical-polarity motors, motor number had minimal affect on directional velocity, whereas ensembles of opposite-polarity motors engaged in a tug-of-war resolvable by disengaging one motor species.

Vibratory responses of synthetic, self-oscillating vocal fold models

The flow-induced responses of four self-oscillating synthetic vocal fold models are compared. All models were life-sized and fabricated using flexible silicone compounds with material properties comparable to those of human vocal fold tissue. Three of the models had two layers of different stiffness to represent the body-cover grouping of vocal fold tissue. Two of the two-layer models were based on the "M5" geometry [Scherer et al., J. Acoust. Soc. Am. 109, 1616-1630 (2001)], while the third was based on magnetic resonance imaging data. The fourth model included several layers, including a thin epithelial layer, an exceedingly flexible superficial lamina propria layer, a ligament layer that included an anteriorly-posteriorly oriented fiber to restrict vertical motion, and a body layer. Measurements were performed with these models in full larynx and hemilarynx configurations. Data included onset pressure, vibration frequency, glottal flow rate, maximum glottal width, and medial surface motion, the latter two of which were acquired using high-speed imaging techniques. The fourth, multi-layer model exhibited onset pressure, frequency, and medial surface motion traits that are comparable to published human vocal fold data. Importantly, the model featured an alternating convergent-divergent glottal profile and mucosal wave-like motion, characteristics which are important markers of human vocal fold vibration.

Ventricular pressures in phonating excised larynges

Pressure in the laryngeal ventricle was measured with a beveled needle connected to a pressure transducer in excised canine larynges. Air pressures within the ventricle were obtained for different adduction levels of the true vocal folds (TVFs), false vocal folds (FVFs), and subglottal pressures (Ps). Results indicated that the air pressures in the ventricle appear to be strongly related to the motion of the FVFs rather than to the effects of TVF vibration. Both dc and ac pressures depend on FVF adduction, amplitude of motion of the FVFs, and whether the FVFs touch each other during the vibratory cycle. Mean and peak-to-peak pressures in the ventricle were as high as 65% of the mean and peak-to-peak Ps, respectively, when the FVFs vibrated with large amplitude and contact each cycle. If the glottis was not closed, a medial movement of the FVFs appeared to create a positive pressure pulse on the Ps signal due to an increase in the laryngeal flow resistance. The electroglottograph signal showed evidence of tissue contact for both the TVFs and the FVFs. The study suggests that the laryngeal ventricle acts as a relatively independent aero-acoustic chamber that depends primarily upon the motion of the FVFs.

Real-time optical gating for three-dimensional beating heart imaging

We demonstrate real-time microscope image gating to an arbitrary position in the cycle of the beating heart of a zebrafish embryo. We show how this can be used for high-precision prospective gating of fluorescence image slices of the moving heart. We also present initial results demonstrating the application of this technique to 3-D structural imaging of the beating embryonic heart.

Quantitative study of vibrational symmetry of injured vocal folds via digital kymography in excised canine larynges

PURPOSE

Digital kymography and vocal fold curve fitting are blended with detailed symmetry analysis of kymograms to provide a comprehensive characterization of the vibratory properties of injured vocal folds.

METHOD

Vocal fold vibration of 12 excised canine larynges was recorded under uninjured, unilaterally injured, and bilaterally injured conditions. Kymograms were created at 25%, 50%, and 75% of the vocal fold length, and vibratory parameters were compared quantitatively among conditions and were studied with respect to right-left and anterior-posterior symmetries.

RESULTS

Anterior-posterior amplitude asymmetry was found in the bilateral condition. The unilateral condition showed significant right-left amplitude asymmetry, and it showed the lowest right-left phase symmetry among the conditions. In condition comparisons, vertical phase difference did not show significant differences among conditions, whereas amplitudes were significantly different among conditions at all line scan positions and most vocal fold lips. Significant differences in frequency were found among the conditions at all 4 vocal fold lips, with the bilateral condition exhibiting the greatest frequency.

CONCLUSION

Digital kymography and curve fitting provide detailed information about the vibratory behavior of injured vocal folds. Awareness of vibratory properties associated with vocal fold injury may aid in diagnosis, and the quantitative abilities of digital kymography may allow for objective treatment selection.

An automatic apparatus for repeated stimulation of isolated organs by agonist drugs

A simple commutator for attachment to a standard laboratory kymograph has been designed to operate automatically an apparatus for producing repeated contractions of isolated organs by agonist drugs.

Probing intracellular motor protein activity using an inducible cargo trafficking assay

Although purified cytoskeletal motor proteins have been studied extensively with the use of in vitro approaches, a generic approach to selectively probe actin and microtubule-based motor protein activity inside living cells is lacking. To examine specific motor activity inside living cells, we utilized the FKBP-rapalog-FRB heterodimerization system to develop an in vivo peroxisomal trafficking assay that allows inducible recruitment of exogenous and endogenous kinesin, dynein, and myosin motors to drive specific cargo transport. We demonstrate that cargo rapidly redistributes with distinct dynamics for each respective motor, and that combined (antagonistic) actions of more complex motor combinations can also be probed. Of importance, robust cargo redistribution is readily achieved by one type of motor protein and does not require the presence of opposite-polarity motors. Simultaneous live-cell imaging of microtubules and kinesin or dynein-propelled peroxisomes, combined with high-resolution particle tracking, revealed that peroxisomes frequently pause at microtubule intersections. Titration and washout experiments furthermore revealed that motor recruitment by rapalog-induced heterodimerization is dose-dependent but irreversible. Our assay directly demonstrates that robust cargo motility does not require the presence of opposite-polarity motors, and can therefore be used to characterize the motile properties of specific types of motor proteins.

Analysis of vesicular trafficking in primary neurons by live imaging

Alzheimer's disease, the most common neurodegenerative disease, is characterized by a progressive loss of synapses and accumulation of amyloid-beta (Aβ) peptides in the brain. Previous studies demonstrated that acute increase in synaptic activity in cultured hippocampal slices and mouse brains (Cirrito et al. Neuron 48: 913-922, 2005; Kamenetz et al. Neuron 37: 925-937, 2003) enhanced secretion of Aβ. Since synaptic activity promotes Aβ secretion, it could also affect the trafficking and processing of its precursor, the amyloid precursor protein (APP). Here, we describe a method to investigate the effect of acute synaptic activation on APP trafficking within dendrites.

Vocal fold and ventricular fold vibration in period-doubling phonation: physiological description and aerodynamic modeling

Occurrences of period-doubling are found in human phonation, in particular for pathological and some singing phonations such as Sardinian A Tenore Bassu vocal performance. The combined vibration of the vocal folds and the ventricular folds has been observed during the production of such low pitch bass-type sound. The present study aims to characterize the physiological correlates of this acoustical production and to provide a better understanding of the physical interaction between ventricular fold vibration and vocal fold self-sustained oscillation. The vibratory properties of the vocal folds and the ventricular folds during phonation produced by a professional singer are analyzed by means of acoustical and electroglottographic signals and by synchronized glottal images obtained by high-speed cinematography. The periodic variation in glottal cycle duration and the effect of ventricular fold closing on glottal closing time are demonstrated. Using the detected glottal and ventricular areas, the aerodynamic behavior of the laryngeal system is simulated using a simplified physical modeling previously validated in vitro using a larynx replica. An estimate of the ventricular aperture extracted from the in vivo data allows a theoretical prediction of the glottal aperture. The in vivo measurements of the glottal aperture are then compared to the simulated estimations.

[The ultra-rapid cinematography of the larynx, its contributions in speech pathology]

The development in the medical field of high speed cinematography and its dissemination in the field of speech pathology will probably change the way we view the larynx and diagnose its disorders. So far only the stroboscope could inform us about the appearance of vocal cord vibration but with certain limitations. Indeed the wave motion of the vocal cords is really only apparent motion. It is made possible through the phenomenon of retinal persistence of images and light intermittent vocal folds set to the frequency of the voice and out of phase by a few Hertz. This technique has several disadvantages: The need for the voice to trigger the strobe light; a low number of frames per second (25 fps) recorded; frame loss for the period between unlit two flashes; limitation in the study of the upper voice spectrum (gearing). The ultra-rapid cinematography brings a big difference in design since the digital recording can shoot up to 4000 frames per second with permanent lighting of the larynx. The slow reading of short sequences permits us to view the actual movement of vibrating structures, and to analyze the behavior of the vibrator during the transitional phases of the attack, depreciation and termination of sound. The footage in high resolution permits a detailed analysis of the movements of opening and closing of the vocal cords in phonation and respiration, and the diagnosis of lesions.

Investigation of voice initiation and voice offset characteristics with high-speed digital imaging

This study involves preliminary investigation of the characteristics of the voice initiation period (VIP) and voice offset period (VOP) using high-speed digital imaging. The goals of the study were to develop a methodology to objectively analyze these periods of phonation and to explore the feasibility of studying the effects of aging on these phonation segments. Results of the analysis of the data from two female subjects, one younger and one older, with the developed methodology, demonstrated that the older subject's VIP was characterized by a slow and irregular increase in glottal area waveform (GAW) until reaching 90% of the maximum opening of the glottis at 244 frames or 122 ms. The younger subject demonstrated a sharp increase in GAW during VIP, taking only 155 frames or 77.5 ms to reach the 90% mark. Also, the older subject took a greater number of frames for the vocal fold vibration to come to a complete stop than the younger subject during the VOP; 275 frames and 150 frames respectively.

Videokymographic analysis of patients after frontolateral laryngectomy with sternohyoid muscle flap reconstruction

A retrospective study was conducted to analyse videokymographic findings from patients who underwent vertical frontolateral laryngectomy with reconstruction using a sternohyoid muscle flap. Overall, 22 patients with T1b and T2 glottic tumours and more than one year of follow-up were studied. Two experienced observers analysed the recorded videokymographic data. A cross-sectional descriptive design was used. The images showed the vocal vibratory behaviour during sustained /i/ phonation. The vibratory source was supraglottic in 7/22 patients, glottic in 11 and mixed in 4. The mean duration of the glottic cycles extracted from the supraglottic, mixed and glottic vibratory sources was 6.4 ms, 5 ms and 4.6 ms, corresponding to the fundamental frequency (f0) of 188.7 Hz, 200 Hz and 215.7 Hz, respectively. Of the 11 patients with a glottic vibratory source, 4 did not present a closed phase in the glottic cycle. The mean open quotient was 79%, 40% and 63%, for the supraglottic, mixed and glottic vibratory sources, respectively. All 11 reconstructed vocal cords presented a rounded lateral peak. Of the 15 preserved vocal cords, 11 presented a rounded lateral peak and 4 had sharp peaks. All patients with a glottic vibratory source presented a rounded medial peak. All the vocal cords evaluated presented a mucosal wave, which was normal in 3 patients with a glottic source and clearly reduced in the others. Only one case presented phase asymmetry. The mean values for the amplitude asymmetry index were 0.92 and 0.68, for the mixed and supraglottic vibratory sources, respectively.

Anterograde microtubule transport drives microtubule bending in LLC-PK1 epithelial cells

Microtubules (MTs) have been proposed to act mechanically as compressive struts that resist both actomyosin contractile forces and their own polymerization forces to mechanically stabilize cell shape. To identify the origin of MT bending, we directly observed MT bending and F-actin transport dynamics in the periphery of LLC-PK1 epithelial cells. We found that F-actin is nearly stationary in these cells even as MTs are deformed, demonstrating that MT bending is not driven by actomyosin contractility. Furthermore, the inhibition of myosin II activity through the use of blebbistatin results in microtubules that are still dynamically bending. In addition, as determined by fluorescent speckle microscopy, MT polymerization rarely results, if ever, in bending. We suppressed dynamic instability using nocodazole, and we observed no qualitative change in the MT bending dynamics. Bending most often results from anterograde transport of proximal portions of the MT toward a nearly stationary distal tip. Interestingly, we found that in an in vitro kinesin-MT gliding assay, MTs buckle in a similar manner. To make quantitative comparisons, we measured curvature distributions of observed MTs and found that the in vivo and in vitro curvature distributions agree quantitatively. In addition, the measured MT curvature distribution is not Gaussian, as expected for a thermally driven semiflexible polymer, indicating that thermal forces play a minor role in MT bending. We conclude that many of the known mechanisms of MT deformation, such as polymerization and acto-myosin contractility, play an inconsequential role in mediating MT bending in LLC-PK1 cells and that MT-based molecular motors likely generate most of the strain energy stored in the MT lattice. The results argue against models in which MTs play a major mechanical role in LLC-PK1 cells and instead favor a model in which mechanical forces control the spatial distribution of the MT array.

An automatic method to quantify mucosal waves via videokymography

OBJECTIVE/HYPOTHESIS

Vocal fold vibration is associated with four distinct vibratory patterns: those of the right-upper, right-lower, left-upper, and left-lower vocal fold lips. The purpose of this study was to propose a least squares method to quantify the vibratory properties of each of the four vocal fold lips via videokymography (VKG).

STUDY DESIGN

This was a methodological study designed to examine the impact of subglottal pressure and line-scan position on mucosal wave parameters.

METHODS

VKG, a line-scan imaging technique, has proven to be an effective method for studying vocal fold vibratory patterns. This study used VKG images and an automatic mucosal wave extraction method to examine the vibration of each individual vocal fold lip of 17 excised canine larynges under differing subglottal pressures and line-scan positions.

RESULTS

Varying subglottal pressure led to results consistent with previous studies. Examination of the vocal folds at different line-scan positions along its length revealed that amplitude is greatest at the midpoint of the vocal fold, followed by the anterior portion of the vocal fold, with the posterior portion having the lowest amplitude (P < .001). Frequency and phase delay did not change significantly throughout the length of the vocal fold.

CONCLUSIONS

The method used in this study allows for easy determination of four sets of vibratory parameters, and examination of the effect of biomechanical parameters on vocal fold vibrations.

Intraflagellar transport (IFT) during assembly and disassembly of Chlamydomonas flagella

Intraflagellar transport (IFT) of particles along flagellar microtubules is required for the assembly and maintenance of eukaryotic flagella and cilia. In Chlamydomonas, anterograde and retrograde particles viewed by light microscopy average 0.12-microm and 0.06-microm diameter, respectively. Examination of IFT particle structure in growing flagella by electron microscopy revealed similar size aggregates composed of small particles linked to each other and to the membrane and microtubules. To determine the relationship between the number of particles and flagellar length, the rate and frequency of IFT particle movement was measured in nongrowing, growing, and shortening flagella. In all flagella, anterograde and retrograde IFT averaged 1.9 microm/s and 2.7 microm/s, respectively, but retrograde IFT was significantly slower in flagella shorter than 4 mum. The number of flagellar IFT particles was not fixed, but depended on flagellar length. Pauses in IFT particle entry into flagella suggest the presence of a periodic "gate" that permits up to 4 particles/s to enter a flagellum.

Strobovideolaryngoscopy and Laboratory Voice Evaluation

A complete and thorough vocal history and physical examination is the cornerstone of the evaluation of any patient who has a vocal complaint. Continued scientific progress in the understanding of vocal fold vibration and sound production combined with advances in technology have resulted in the availability of numerous supplemental diagnostic laboratory tools for an optimal voice evaluation. This article presents additional clinical tools accessible to the otolaryngologist that may aid in diagnosis and help elucidate difficult vocal tract pathology.

Coronin 1B coordinates Arp2/3 complex and cofilin activities at the leading edge

Actin filament formation and turnover within the treadmilling actin filament array at the leading edge of migrating cells are interdependent and coupled, but the mechanisms coordinating these two activities are not understood. We report that Coronin 1B interacts simultaneously with Arp2/3 complex and Slingshot (SSH1L) phosphatase, two regulators of actin filament formation and turnover, respectively. Coronin 1B inhibits filament nucleation by Arp2/3 complex and this inhibition is attenuated by phosphorylation of Coronin 1B at Serine 2, a site targeted by SSH1L. Coronin 1B also directs SSH1L to lamellipodia where SSH1L likely regulates Cofilin activity via dephosphorylation. Accordingly, depleting Coronin 1B increases phospho-Cofilin levels, and alters lamellipodial dynamics and actin filament architecture at the leading edge. We conclude that Coronin 1B's coordination of filament formation by Arp2/3 complex and filament turnover by Cofilin is required for effective lamellipodial protrusion and cell migration.

Dispersal of epithelial cancer cell colonies by lysophosphatidic acid (LPA)

We describe a model system in which cancer cell colonies disperse into single, highly migratory cells in response to lysophosphatidic acid (LPA). Though LPA is known to stimulate chemotaxis and chemokinesis, a colony dispersal effect has not been reported, to our knowledge. Cancer colony dispersal by LPA is comprised of an ordered sequence of events: (1) stimulation of membrane ruffling and formation of lamellipodia, (2) dissolution of adherens junctions, (3) single cell migration in a mesenchymal-like morphology we term "ginkgo-leaf." The net result is dispersal of carcinoma cells from a compact colony. We analyzed these three steps using live-cell imaging and computer-assisted quantification and measured the following parameters: onset of lamellipodia formation, lamellipodia velocity, colony dispersal, trans-epithelial resistance, migrating cell number and speed. Because hepatocyte growth factor (HGF) was described as an epithelial scatter factor, we compared it to LPA in our system and found that HGF has no epithelial colony dispersal properties and that this effect is strictly related to LPA. Given its striking similarity to tumor cell budding observed in patients, we propose that LPA-colony dispersal may provide a cellular mechanism underlying cancer invasion and as such deserves further studies.

Cortactin promotes cell motility by enhancing lamellipodial persistence

BACKGROUND

Lamellipodial protrusion, which is the first step in cell movement, is driven by actin assembly and requires activity of the Arp2/3 actin-nucleating complex. However, it is unclear how actin assembly is dynamically regulated to support effective cell migration.

RESULTS

Cells deficient in cortactin have impaired cell migration and invasion. Kymography analyses of live-cell imaging studies demonstrate that cortactin-knockdown cells have a selective defect in the persistence of lamellipodial protrusions. The motility and protrusion defects are fully rescued by cortactin molecules, provided both the Arp2/3 complex and F-actin binding sites are intact. Consistent with this requirement for simultaneous contacts with Arp2/3 and F-actin, cortactin is recruited by Arp2/3 complex to lamellipodia and binds with a higher affinity to ATP/ADP-Pi-F-actin than to ADP-F-actin. In situ labeling of lamellipodia revealed that the relative levels of free barbed ends of actin filaments are reduced by over 30% in the cortactin-knockdown cells; however, there is no change in Arp2/3-complex localization to lamellipodia. Cortactin-knockdown cells also have a selective defect in the assembly of new adhesions in protrusions, as assessed by analysis of GFP-paxillin dynamics in living cells.

CONCLUSIONS

Cortactin enhances lamellipodial persistence, at least in part through regulation of Arp2/3 complex. The presence of cortactin also enhances the rate of new adhesion formation in lamellipodia. In vivo, these functions may be important during directed cell motility.

Interactions between CLIP-170, tubulin, and microtubules: implications for the mechanism of Clip-170 plus-end tracking behavior

CLIP-170 belongs to a group of proteins (+TIPs) with the enigmatic ability to dynamically track growing microtubule plus-ends. CLIP-170 regulates microtubule dynamics in vivo and has been implicated in cargo-microtubule interactions in vivo and in vitro. Though plus-end tracking likely has intimate connections to +TIP function, little is known about the mechanism(s) by which this dynamic localization is achieved. Using a combination of biochemistry and live cell imaging, we provide evidence that CLIP-170 tracks microtubule plus-ends by a preassociation, copolymerization, and regulated release mechanism. As part of this analysis, we find that CLIP-170 has a stronger affinity for tubulin dimer than for polymer, and that CLIP-170 can distinguish between GTP- and GDP-like polymer. This work extends the previous analysis of CLIP-170 behavior in vivo and complements the existing fluorescence microscope characterization of CLIP-170 interactions with microtubules in vitro. In particular, these data explain observations that CLIP-170 localizes to newly polymerized microtubules in vitro but cannot track microtubule plus-ends in vitro. These observations have implications for the functions of CLIP-170 in regulating microtubule dynamics.